Extended Data Fig. 9: MSE of CpGs compared to non CpG sites on chromosome 21 and 22.
From: Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies
The mutation rate at CpG sites is more than an order of magnitude greater than non-CpG sites, and thus have a higher rate of recurrent mutations (Wohns, 2022). To evaluate how disregarding recurrent mutation effects overall accuracy (see Methods), we examined the MSE of CpG sites vs. non-CpG sites on the 40 LD blocks of chromosomes 21 and 22 between the LDGM precision matrix and sample correlation matrices. The lower whisker, lower hinge, center, upper hinge and upper whisker correspond to (lower hinge − 1.5× interquartile range (IQR)) and the 25th percentile, median, 75th percentile, and (upper hinge + 1.5× IQR), respectively. For numerical results, see Supplementary Table 13.
